RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bam2graph_8cpp_source.html below:

NCBI C++ ToolKit: src/sra/app/bam2graph/bam2graph.cpp Source File

60 virtual void Init

(

void

);

61 virtual int Run

(

void

);

62 virtual void Exit

(

void

);

73 #define BAM_DIR "1000genomes/ftp/data" 74 #define CONFIG_FILE_NAME "analysis.bam.cfg" 82

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

83 "CArgDescriptions demo program"

);

85

arg_desc->AddOptionalKey(

"srz"

86 "SRZ accession config file" 87 " (-log and -int options are ignored)"

89

arg_desc->AddOptionalKey(

"file"

"File"

92

arg_desc->AddOptionalKey(

"dir"

"Dir"

93 "BAM files files directory"

95

arg_desc->AddOptionalKey(

"odir"

"OutputDir"

96 "Destination directory"

99

arg_desc->AddOptionalKey(

"ref_label"

"RefLabel"

100 "RefSeq id in BAM file"

102

arg_desc->AddOptionalKey(

"seq_id"

"SeqId"

105

arg_desc->AddOptionalKey(

"delta"

"Delta"

106 "Delta-ext in text ASN.1"

108

arg_desc->AddOptionalKey(

"delta_file"

"DeltaFile"

109 "File with Delta-ext in text ASN.1"

112

arg_desc->AddFlag(

"estimated"

"Make estimated graph using index only"

);

113

arg_desc->AddFlag(

"raw-access"

"Make graph using raw access to BAM"

);

114

arg_desc->AddOptionalKey(

"min_quality"

"MinMapQuality"

115 "Minimal alignment map quality"

117

arg_desc->AddFlag(

"log"

"Generate logarithmic graph"

);

118

arg_desc->AddFlag(

"int"

"Generate graph with int values"

);

119

arg_desc->AddOptionalKey(

"max"

"OutlierMax"

120 "Factor over average to treat as outlier"

122

arg_desc->AddFlag(

"max_details"

"Include detailed outlier info"

);

123

arg_desc->AddOptionalKey(

"bin_size"

"BinSize"

124 "Seq-graph bin size"

126

arg_desc->AddOptionalKey(

"annot_name"

127 "Annot name with generated Seq-graph"

129

arg_desc->AddOptionalKey(

"title"

"Title"

130 "Title of generated Seq-graph"

133

arg_desc->AddDefaultKey(

"o"

"OutputFile"

134 "Output file of ASN.1"

137

arg_desc->AddFlag(

"b"

"Write binary ASN.1"

);

138

arg_desc->AddFlag(

"annot"

"Write Seq-annot only"

);

157 if

( args[

"file"

] ) {

160 else if

( args[

"srz"

] ) {

180 if

( args[

"dir"

] ) {

181

dir = args[

"dir"

].AsString();

186 ITERATE

( vector<string>, it, reps ) {

196 if

( !

CFile

(path).Exists() ) {

199 if

( tt.size() > 0 ) {

208 if

( args[

"ref_label"

] ) {

209

ref_label = args[

"ref_label"

].AsString();

214 if

( tt.size() > 1 ) {

224 if

( args[

"seq_id"

] ) {

225 CSeq_id

seq_id(args[

"seq_id"

].AsString());

232 if

( args[

"annot_name"

] ) {

235 if

( args[

"title"

] ) {

238 if

( args[

"min_quality"

] ) {

241 if

( args[

"log"

] ) {

244 if

( args[

"int"

] ) {

247 if

( args[

"bin_size"

] ) {

250 if

( args[

"max"

] ) {

253 if

( args[

"max_details"

] ) {

256 if

( args[

"estimated"

] ) {

259 if

( args[

"raw-access"

] ) {

263 if

( args[

"delta"

] ) {

265 string

s = args[

"delta"

].AsString();

267

s =

"Delta-ext ::= "

+s;

272 else if

( args[

"delta_file"

] ) {

287 if

( 0 && args[

"estimated"

] ) {

302 CBamDb

bam(mgr, path, path+

".bai"

);

313 if

( args[

"annot"

] ) {

326 if

(

CFile

(srz_name).IsDir() ) {

330 if

( args[

"dir"

] ) {

331

dir = args[

"dir"

].AsString();

337 if

( args[

"odir"

] ) {

338

odir = args[

"odir"

].AsString();

351

vector<string> tokens;

354 while

( getline(srz, line) ) {

357 if

( tokens.size() < 4 ) {

360 string

ref_label = tokens[0];

361 string

acc = tokens[1];

363 if

( tokens[2].

empty

() ) {

369 string

bam_name = tokens[3];

370 if

( tokens.size() < 5 ) {

371 ERR_POST

(

"No coverage requested for "

<<ref_label);

375 string

out_name = tokens[4];

378 LOG_POST

(

"Processing "

<<ref_label<<

" -> "

<<out_path);

383 if

( args[

"bin_size"

] ) {

386 if

( args[

"annot_name"

] ) {

392 if

( args[

"title"

] ) {

398 if

( args[

"min_quality"

] ) {

402 if

( args[

"estimated"

] ) {

405 if

( args[

"raw-access"

] ) {

410 if

( 0 && args[

"estimated"

] ) {

412 if

( bam_path != db_name ) {

414

header.

Read

(bam_path);

415

index.

Read

(bam_path+

".bai"

);

426 if

( bam_path != db_name ) {

429

raw_db =

CBamRawDb

(bam_path, bam_path+

".bai"

);

432

db =

CBamDb

(mgr, bam_path, bam_path+

".bai"

);

464 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

int main(int argc, const char *argv[])

virtual void Exit(void)

Cleanup on application exit.

void ProcessFile(const string &file)

void ProcessSrz(string srz_name)

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

void SetGraphBinSize(TSeqPos bin_size)

void SetRawAccess(bool raw_access=true)

void SetGraphTitle(const string &title)

bool GetEstimated(void) const

make estimated graph using BAM index only the bin size will be derived from index

void SetOutlierMax(double x)

void SetEstimated(bool estimated=true)

const string & GetAnnotName(void) const

Annot name of generated Seq-graph.

void SetGraphValueType(EGraphValueType type)

void SetAnnotName(const string &name)

void SetOutlierDetails(bool details=true)

CRef< CSeq_entry > MakeSeq_entry(CBamMgr &mgr, const string &bam_file, const string &bam_index)

Generate Seq-entry for BAM file.

void SetRefLabel(const string &ref_label)

void SetGraphType(EGraphType type)

void SetRefId(const CSeq_id &ref_id)

const CSeq_id & GetRefId(void) const

Seq-id for the reference sequence in generated entry.

void SetSeq_inst(CRef< CSeq_inst > inst)

Use specified Seq-inst object for the virtual sequence.

void SetMinMapQuality(int qual)

void Read(const string &index_file_name)

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, TIndexLevel min_index_level, TIndexLevel max_index_level) const

const TAnnot & GetAnnot(void) const

std::ofstream out("events_result.xml")

main entry point for tests

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDiag_Info

Informational message.

void Fatal(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

string GetDir(EIfEmptyPath mode=eIfEmptyPath_Current) const

Get the directory component for this directory entry.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

#define MSerial_AsnBinary

#define MSerial_AsnText

I/O stream manipulators â.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

@ eStart

Start timer immediately after creating.

@ e_Gi

GenInfo Integrated Database.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eMol_na

just a nucleic acid

CBioseq_Base_Info & GetBase(CTSE_Info &tse, const CBioObjectId &id)

constexpr bool empty(list< Ts... >) noexcept

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

std::istream & in(std::istream &in_, double &x_)

Int4 delta(size_t dimension_, const Int4 *score_)

Defines location of test data folder at NCBI.

static const char * NCBI_GetTestDataPath(void)

Get the directory where test data is stored at NCBI.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4